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  <div class="section" id="neighborlist">
<h1>NeighborList<a class="headerlink" href="#neighborlist" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="atomman.NeighborList">
<em class="property">class </em><code class="sig-prename descclassname">atomman.</code><code class="sig-name descname">NeighborList</code><span class="sig-paren">(</span><em class="sig-param">**kwargs</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.NeighborList" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<p>Class that finds and stores the neighbor atoms for a system.</p>
<dl class="method">
<dt id="atomman.NeighborList.build">
<code class="sig-name descname">build</code><span class="sig-paren">(</span><em class="sig-param">system</em>, <em class="sig-param">cutoff</em>, <em class="sig-param">initialsize=20</em>, <em class="sig-param">deltasize=10</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.NeighborList.build" title="Permalink to this definition">¶</a></dt>
<dd><p>Builds the neighbor list for a system.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>system</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The system to calculate the neighbor list for.</p></li>
<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a>) – Radial cutoff distance for identifying neighbors.</p></li>
<li><p><strong>initialsize</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – The number of neighbor positions to initially assign to each atom.
Default value is 20.</p></li>
<li><p><strong>deltasize</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)"><em>int</em></a><em>, </em><em>optional</em>) – Specifies the number of extra neighbor positions to allow each atom
when the number of neighbors exceeds the underlying array size.
Default value is 10.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.NeighborList.coord">
<em class="property">property </em><code class="sig-name descname">coord</code><a class="headerlink" href="#atomman.NeighborList.coord" title="Permalink to this definition">¶</a></dt>
<dd><p>The atomic coordination numbers</p>
</dd></dl>

<dl class="method">
<dt id="atomman.NeighborList.dump">
<code class="sig-name descname">dump</code><span class="sig-paren">(</span><em class="sig-param">fname</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.NeighborList.dump" title="Permalink to this definition">¶</a></dt>
<dd><p>Saves the neighbor list to a file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>fname</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a>) – The file name to save the content to.</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.NeighborList.load">
<code class="sig-name descname">load</code><span class="sig-paren">(</span><em class="sig-param">model</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.NeighborList.load" title="Permalink to this definition">¶</a></dt>
<dd><p>Read in a neighbor list from a file.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em> or </em><em>file-like object</em>) – Gives the file path or content to load.</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.NeighborList.nlist">
<em class="property">property </em><code class="sig-name descname">nlist</code><a class="headerlink" href="#atomman.NeighborList.nlist" title="Permalink to this definition">¶</a></dt>
<dd><p>The underlying numpy array of coord + neighbor ids</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>numpy.ndarray</p>
</dd>
</dl>
</dd></dl>

</dd></dl>

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